Contacts of the strand formed by residues 372 - 379 (chain G) in PDB entry 2HU4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 372 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365G THR* 3.6 1.8 - - - -
366G LYS* 2.9 22.7 + - - +
367G SER* 3.2 17.1 + - - -
370G SER* 2.8 28.1 + - - -
371G ARG* 1.3 70.8 - - - +
373G GLY* 1.3 63.4 + - - +
400G ILE* 3.4 23.1 + - - -
402G ASP 3.7 5.6 - - - -
403G TRP* 3.4 22.1 - - - +
404G SER* 3.6 0.4 + - - -
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Residues in contact with GLY 373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365G THR* 3.3 8.1 - - - -
366G LYS* 3.7 5.8 - - - -
372G SER* 1.3 74.8 - - - +
374G PHE* 1.3 62.0 + - - +
398G VAL* 3.3 7.6 - - - -
399G ALA 3.0 25.7 + - - -
400G ILE* 4.1 2.2 - - - -
402G ASP 2.7 16.6 + - - -
404G SER* 2.8 23.5 + - - -
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Residues in contact with PHE 374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352G PHE* 4.0 2.5 - + - -
363G GLY* 3.5 24.2 - - - -
364G ARG* 3.1 30.3 - - - -
365G THR* 4.1 4.7 - - + +
366G LYS* 3.9 6.8 + - - +
373G GLY* 1.3 76.4 - - - +
375G GLU* 1.3 83.6 + - - +
376G MET* 4.0 2.2 - - - -
397G ILE* 3.1 35.6 + - + -
398G VAL* 2.9 35.5 + - + +
404G SER* 4.6 6.7 - - - -
405G GLY 4.9 4.5 - - - -
407G SER* 3.6 34.1 - - - -
422G PHE* 3.8 21.8 - + - -
424G VAL* 3.9 15.9 - - + -
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Residues in contact with GLU 375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327G ARG* 4.9 0.7 + - - -
362G ILE 3.7 0.7 - - - +
363G GLY* 3.4 3.8 - - - -
364G ARG* 2.9 70.9 + - + +
365G THR 4.4 2.2 - - - +
366G LYS* 3.0 28.2 + - + +
374G PHE* 1.3 80.3 - - - +
376G MET* 1.3 64.8 - - - +
377G ILE* 3.1 15.8 - - + +
394G LYS* 2.8 40.1 + - + -
395G GLN 3.3 12.6 - - - +
396G ASP* 4.5 2.0 - - - +
397G ILE 4.2 1.6 - - - +
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Residues in contact with MET 376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G TRP* 3.5 53.8 - - + +
352G PHE* 3.7 29.6 - - + -
361G TRP* 4.0 15.1 - - + -
362G ILE 3.3 8.3 - - - +
363G GLY* 3.4 20.6 - - - +
374G PHE* 4.0 2.9 - - - -
375G GLU* 1.3 74.6 - - - +
377G ILE* 1.3 61.2 + - - +
392G VAL 3.9 0.3 - - - +
394G LYS* 3.3 3.8 - - - -
395G GLN* 2.8 43.2 + - + +
397G ILE* 3.9 8.7 - - + -
422G PHE* 3.7 26.2 - - + -
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Residues in contact with ILE 377 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321G VAL* 3.8 11.9 - - + -
360G VAL 3.4 2.1 - - - +
361G TRP* 3.2 6.5 - - - -
362G ILE* 2.7 51.3 + - + +
364G ARG* 3.5 28.5 - - + +
375G GLU* 3.1 34.1 - - + +
376G MET* 1.3 79.0 - - - +
378G TRP* 1.3 62.3 + - - +
379G ASP* 3.8 2.6 + - + +
390G PHE* 3.5 40.2 - - + -
392G VAL 3.4 5.4 - - - +
394G LYS* 4.3 13.2 - - + +
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Residues in contact with TRP 378 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356G TYR* 4.0 25.6 - + + -
359G GLY* 4.0 15.7 - - - -
360G VAL* 3.5 30.1 - - - -
361G TRP* 3.3 57.8 - + + -
377G ILE* 1.3 71.4 - - - +
379G ASP* 1.3 58.9 + - - +
380G PRO* 3.7 28.6 - - + +
390G PHE* 3.4 3.1 - - - +
391G SER* 2.9 46.2 + - - -
392G VAL* 2.8 25.3 + - + +
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Residues in contact with ASP 379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319G SER* 2.4 37.7 + - - +
321G VAL* 5.0 1.6 - - + -
360G VAL* 2.9 37.8 + - + +
362G ILE* 4.8 6.3 - - + -
377G ILE* 3.8 2.4 + - + -
378G TRP* 1.3 73.8 - - - +
380G PRO* 1.3 87.9 - - - +
381G ASN 4.1 1.0 - - - +
382G GLY* 3.0 15.6 + - - -
385G GLU 4.9 0.5 - - - +
387G ASP* 4.2 7.3 - - - +
389G SER* 3.1 23.3 + - - +
390G PHE* 4.0 9.0 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il